Check each branch against its own Bioconductor version - #502
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* Drop the `ubuntu-latest` Bioconductor release leg from the matrix * Derive `bioc-version` from the target branch instead of the matrix * Run the workflow on pushes to `RELEASE_**` as well as `devel`
`RELEASE_3_22` needs Bioconductor 3.22 and R 4.5, not whichever release happens to be current. Derive the version from the branch name in a small `bioc-version` job and feed it to the matrix.
rcannood
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RELEASE_ branches against Bioconductor release
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Bencher Report| Project | anndataR |
| Branch | ci/bioc-version-from-branch |
| Testbed | ubuntu-latest |
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lazappi
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This was referenced Aug 15, 2026
rcannood
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* Check each branch against its own Bioconductor version (#502) * check RELEASE_ branches against bioc release * Drop the `ubuntu-latest` Bioconductor release leg from the matrix * Derive `bioc-version` from the target branch instead of the matrix * Run the workflow on pushes to `RELEASE_**` as well as `devel` * add NEWS entry * pin each RELEASE_ branch to its own bioc version `RELEASE_3_22` needs Bioconductor 3.22 and R 4.5, not whichever release happens to be current. Derive the version from the branch name in a small `bioc-version` job and feed it to the matrix. (cherry picked from commit 8320a69) * Add support for `nullable-string-array` (#480) * Add read_h5ad_nullable_string() helper * Add read_zarr_nullable_string() * Add write_h5ad_nullable_string() * Add write_zarr_nullable_string() * Update example files * Update example data files * Add tests for nullable strings * Use zarr_format * Add nullable string roundtrip tests * Style * Update NEWS --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> (cherry picked from commit c5cf4be) * Keep running BiocCheck on release branches PR #502 dropped the `ubuntu-latest` + Bioconductor devel matrix leg and gated BiocCheck on the resolved version being `devel`. On a `RELEASE_*` branch that version is now `3.23`, so BiocCheck stopped running there entirely. Run it on `ubuntu-latest` regardless of the resolved version; every branch is checked against the Bioconductor version it targets, so BiocCheck is meaningful on both. `devel` needs the same change. * Update NEWS and bump version to 1.2.2 * Fix logical matrices losing their shape when written to H5AD hdf5_write_boolean_dataset() called as.integer(value) before checking dim(value) to compute the dataspace shape. as.integer() drops the dim attribute, so the check always fell through to the flat-vector branch, and any 2D+ logical matrix (X/layers/obsm/varm) was written as a 1D dataset. Reading it back then failed since the shape no longer matched (n_obs, n_var). Capture dims before the conversion, and align H5Screate_simple()'s native argument with hdf5_write_dataset() a few lines above (native = FALSE), which is what write_h5ad_dense_array() already transposes values for. Fixes #495 (cherry picked from commit fa91217) * Add PR #496 to the NEWS entry for 1.2.2 --------- Co-authored-by: Luke Zappia <lazappi@users.noreply.github.com> Co-authored-by: Juan Andrés Tejedor <jatejser@doctor.upv.es>
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Related to: the
ubuntu-latest (release)check that has been red ondevelsince #455Description
Checking
develagainst Bioconductor release was never going to work whiledeveldepends on devel-only packages. This PR derives the Bioc version from the branch.
The r-universe checks don't make this workflow redundant atm, since the runner has no
h5diffandskips the byte-level roundtrip comparisons in
test-roundtrip-*.R.We'll want to backport this to the release branches
Checklist
Before review
Before merge
NEWS